Stars
Repository to host tool-specific module files for the Nextflow DSL2 community!
BioinfoTongLI / Image-ST
Forked from cellgeni/Image-STA pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.
Nextflow module to use Baysor for cell segmentation in imaging-based Spatial Transcriptomics
Segment Anything for Microscopy
A simple plugin for an interactive visualization of spatial omics data.
Example tutorial for setting up a jupyter desktop remote proxy with napari.
Bayesian Segmentation of Spatial Transcriptomics Data
A python extension for the automatic alignment of a source image or a stack (movie) to a target image/reference frame.
Code to go along the lecture course "Advanced Machine Learning for Physics, Science, and Artificial Scientific Discovery"
python library for particles tracking in 2D+t and 3D+t scientific images
starfish: unified pipelines for image-based transcriptomics
A tutorial on performing spot detection using napari, scikit-image, and scipy
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
napari: a fast, interactive, multi-dimensional image viewer for python
Ongoing work on cell motility system for the CPM using Morpheus, FitMultiCell, and Python
Contains code and morpheus files used as a FitMultiCell tutorial for parameter estimation and model selection.
General working directory for Machine Learning projects.